MRG: Merge branch main into features/melinatorcosiupdates

bin/mcosima

@@ -392,6 +392,7 @@ echo "TAGS=( )" >> ${KillFileName}
 
 
 # Start the sims
+FirstTag=""
 for (( i=1; i <= ${Threads}; i+=1 )); do
   # First check if we are ready to launch a new thread
   mwait -i=${Max} -p=cosima
@@ -429,6 +430,10 @@ for (( i=1; i <= ${Threads}; i+=1 )); do
   sleep ${Delay}
 
   echo "TAGS+=( ${Tag} )"  >> ${KillFileName}
+
+  if [[ ${FirstTag} == "" ]]; then
+    FirstTag=${Tag}
+  fi
 done
 
 cat  >> ${KillFileName} <<EOF
@@ -477,10 +482,33 @@ if [[ ${Concatenate} == yes ]]; then
     fi
 
     # Wait until the first such file is created
-    while ( test ! -f ${FirstFileName} ); do
-      sleep 1
-      echo "Waiting for the simulation file \"${FirstFileName}\" to appear ..."
-    done
+    FirstPID=$(ps -Af | grep "[ ]${FirstTag}" | grep -v "bash -c " | awk '{ print $2 }')
+    if [[ ${FirstPID} == "" ]] && [ ! -f ${FirstFileName} ]; then
+      echo ""
+      echo "Error:"
+      echo "Cosima is not running, and no sim file has been created."
+      echo "Most likely cosima has crashed during startup."
+      echo "Please do a test run with just cosima before running mcosima."
+      echo ""
+      echo "Exiting"
+      exit 1
+    else
+      while [[ ${FirstPID} == "" ]] && [ ! -f ${FirstFileName} ]; do
+        sleep 1
+        echo "Waiting for the simulation file \"${FirstFileName}\" to appear ..."
+        FirstPID=$(ps -Af | grep "[ ]${FirstTag}" | grep -v "bash -c " | awk '{ print $2 }')
+      done
+    fi
+
+    if [ ! -f ${FirstFileName} ]; then
+      echo ""
+      echo "Error:"
+      echo "No sim file has been created."
+      echo "Please do a test run with just cosima before running mcosima,"
+      echo ""
+      echo "Exiting"
+      exit 1
+    fi
 
     # Wait until the header is written
     if [[ "${Zip}" == "yes" ]]; then

bin/megalib-config

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+# Tool to check the configuration used to compile MEGAlib
+
+commandhelp() {
+  echo ""
+  echo "megalib-config";
+  echo "Copyright by Andreas Zoglauer"
+  echo ""
+  echo "Shows MEGAlib configuration options"
+  echo ""
+  echo "Usage: megalib-config [options]";
+  echo ""
+  echo "Options:"
+  echo "  --compiler                : Version of the compiler used during configuration"
+  echo "  --python3                 : Version of python3 used during configuration"
+  echo "  --root                    : Version of ROOT used during configuration"
+  echo "  --geant4                  : Version of Geant4 used during configuration"
+  echo "  --help                    : Show this help"
+  echo ""
+}
+
+
+# Store command line as array
+CMD=( "$@" )
+MACHINESSTRING=""
+
+# Check for help
+for C in "${CMD[@]}"; do
+  if [[ ${C} == --help ]]; then
+    echo ""
+    commandhelp
+    exit 0
+  fi
+done
+
+
+for C in "${CMD[@]}"; do
+  if [[ ${C} == --compiler ]]; then
+    cat $MEGALIB/config/Configuration.txt | grep "COMPILER" | awk -F= '{print $2}'
+  elif [[ ${C} == --python3 ]]; then
+    cat $MEGALIB/config/Configuration.txt | grep "PYTHON3" | awk -F= '{print $2}'
+  elif [[ ${C} == --root ]]; then
+    cat $MEGALIB/config/Configuration.txt | grep "ROOT" | awk -F= '{print $2}'
+  elif [[ ${C} == --geant4 ]]; then
+    cat $MEGALIB/config/Configuration.txt | grep "GEANT4" | awk -F= '{print $2}'
+  elif [[ ${C} == *-h* ]]; then
+    echo ""
+    commandhelp
+    exit 0
+  fi
+done
+
+exit 0

bin/mlines

@@ -21,7 +21,7 @@ cd ${DIR}
 
 CMD=" "
 TOTAL=0
-TYPES="cxx cc f hh h C cpp" 
+TYPES="cxx cc f hh h C cpp sh" 
 for TYPE in ${TYPES}; do
   for FILE in `find . -name "*.${TYPE}"`; do
     LINES=`grep -v '^\s*$' ${FILE} | grep -v '////' | wc -l`

bin/mresponsecreator

@@ -207,6 +207,7 @@ else
       nice -19 responsecreator -f ${SINGLEFILE} -r ${OUT} ${NEWCMD} &> /dev/null &
     fi
     echo "Started run ${COUNTER} out of ${COUNTERMAX} with ID ${ID}"
+    sleep 1
 
     COUNTER=$(( ${COUNTER} + 1 ))
   done

bin/mrevan

@@ -13,6 +13,7 @@ help() {
   echo "    -n <nice>:      The nice level as an integer (default: 0)"
   echo "    -c <file name>: Revan configuration file name (mandatory)"
   echo "    -g <geometry file name>: Overwrites the geometry in the configuration file (optional)"
+  echo "    -o:             Save origin information (for response creation)"
   echo "    -f <file name>: Long list of sim/evta files - MUST BE LAST"
   echo "";
   echo "Example:";
@@ -34,6 +35,7 @@ NICELEVEL=0
 CFG=""
 FILES=""
 GEOMETRY=""
+ORIGIN="FALSE"
 
 # Find the default number of threads
 if [[ ${OSTYPE} == darwin* ]]; then
@@ -56,6 +58,9 @@ while [ $# -gt 0 ] ; do
   -h|--help)
     help;
     exit 0;;
+  -o)
+    ORIGIN="TRUE"
+    ;;
   -t)
     shift;
     if [ $# -eq 0 ]; then
@@ -114,7 +119,7 @@ while [ $# -gt 0 ] ; do
       exit 0;
     fi
     while [ $# -ne 0 ]; do
-      FILES+=" "$1;
+      FILES+="$1 ";
       shift;
     done
     ;;
@@ -165,17 +170,22 @@ echo " "
 echo "Number of threads to use:  ${THREADS}"
 echo "Nice level:                ${NICELEVEL}"
 if [[ ${GEOMETRY} != "" ]]; then
-  echo "Geometry:                ${GEOMETRY}"
+  echo "Geometry:                  ${GEOMETRY}"
 fi
 echo "Revan configuration file:  ${CFG}"
+echo "Origin info:               ${ORIGIN}"
 echo "Sim/evta files:            ${FILES}"
 
 
 # Now run, revan RUN!
 for SIMFILE in ${FILES}; do
   mwait -p=revan -i=${THREADS}
   echo "Launching revan for file ${SIMFILE}"
-  CMD="source ${MEGALIB}/bin/source-megalib.sh; revan -c ${CFG} -a -n -f ${SIMFILE}"
+  OPTIONS="-c ${CFG} -a -n "
+  if [[ ${ORIGIN} == "TRUE" ]]; then
+    OPTIONS+="--oi "
+  fi
+  CMD="source ${MEGALIB}/bin/source-megalib.sh; revan ${OPTIONS} -f ${SIMFILE}"
   if [[ ${GEOMETRY} != "" ]]; then
     CMD+=" -g ${GEOMETRY}"
   fi

config/Makefile.linuxgcc

@@ -9,7 +9,7 @@
 #----------------------------------------------------------------
 
 
-CMODE         = "Linux with gcc and support for C++11"
+CMODE         = "Linux with gcc utilizing C++14"
 DLL           = so
 
 # Basic flags generated by ROOT

configure

@@ -25,6 +25,7 @@ confhelp() {
   echo " "
   echo "--debug=[off/no, on/yes, strong/hard]"
   echo "    Default is on."
+  echo "    Strong enables the address sanitizer on Linux with gcc to detect memory access errors."
   echo " "
   echo "--compiler=[gcc, clang, icc]"
   echo "    This currently only works on Linux. Default is gcc. On a Mac always the default compiler is used."
@@ -483,9 +484,9 @@ if [[ ${DEBUG} == normal ]] || [[ ${DEBUG} == strong ]]; then
   OPTIONS+=" -g"
   if  [[ ${DEBUG} == strong ]]; then
     OPTIONS+=" -DDEBUG1"
-  fi
-  if [[ ${COMP} == gcc ]] && [[ ${OS} == linux ]]; then
-    OPTIONS+=" -fstack-protector-all"
+    if [[ ${COMP} == gcc ]] && [[ ${OS} == linux ]]; then
+      OPTIONS+=" -fsanitize=address"
+    fi
   fi
 fi
 
@@ -623,6 +624,16 @@ echo ""
 echo "Removing old build..."
 make clean
 
+# Store configuration
+echo ""
+echo "Storing configuration..."
+rm -f config/Configuration.txt
+echo "COMPILER=$(gcc --version | head -n 1)" >> config/Configuration.txt
+echo "PYTHON3=$(python3 --version)" >> config/Configuration.txt
+echo "ROOT=$(root-config --version)" >> config/Configuration.txt
+echo "GEANT4=$(geant4-config --version)" >> config/Configuration.txt
+
+
 echo ""
 echo ""
 echo "Done! Now type 'make' to compile and link MEGAlib"

resource/examples/advanced/Atmosphere/make_all.sh

@@ -0,0 +1,6 @@
+
+
+for P in `ls *.cxx`; do
+  make -f ${MEGALIB}/resource/standalone/Makefile.standalone PRG=${P}
+done
+

resource/examples/benchmarks/Benchmark.py

@@ -241,8 +241,12 @@
 FontScaler = 0.5
 
 matplotlib.rcParams.update({'font.size': FontScaler*18})
-matplotlib.rcParams.update({'axes.titlesize': FontScaler*30})
-matplotlib.rcParams.update({'axes.labelsize': FontScaler*24})
+matplotlib.rcParams.update({'axes.titlesize': FontScaler*32})
+matplotlib.rcParams.update({'axes.labelsize': FontScaler*24}) 
+if len(Reference) <= 8:
+  matplotlib.rcParams.update({'xtick.labelsize': FontScaler*18})
+else:
+  matplotlib.rcParams.update({'xtick.labelsize': FontScaler*18*8/len(Reference)})
 matplotlib.rcParams.update({'figure.figsize': [12.0, 6.0]})
 
 x = np.arange(len(Labels))  # the label locations

resource/examples/benchmarks/Benchmark.sh

@@ -20,7 +20,7 @@ checkload() {
 }
 
 
-# For compatibility with macOS Catalina, compile a little C++ program to get the time in milliseconds
+# For compatibility with macOS, compile a little C++ program to get the time in milliseconds
 
 TempEXE=$(mktemp)
 TimerC="${TempEXE}.cpp"
@@ -49,9 +49,12 @@ if [[ $(uname -s) == Linux ]]; then
 
   CPUModel=$( lscpu | grep "Model name" | awk -F: '{print $2 }' | sed -e 's/^[[:space:]]*//' )
   CPUSockets=$( lscpu | grep "Socket" | awk -F: '{print $2 }' | sed -e 's/^[[:space:]]*//' )
-  if ! [[ ${CPUSockets} =~ ^?[0-9]+$ ]]; then
+  if ! [[ ${CPUSockets} =~ ^[0-9]+$ ]]; then
     CPUSockets=1
   fi 
+  if [[ ${CPUSockets} == "0" ]]; then
+    CPUSockets=1
+  fi
   CPUCoresPerSocket=$( lscpu | grep "per socket" | awk -F: '{print $2 }' | sed -e 's/^[[:space:]]*//' )
   if [[ ${CPUCoresPerSocket} == "" ]]; then
     CPUCoresPerSocket=$( lscpu | grep "per cluster" | awk -F: '{print $2 }' | sed -e 's/^[[:space:]]*//' )

resource/examples/benchmarks/References/callisto.bm

@@ -0,0 +1,47 @@
+# Benchmark summary file
+
+HostName:                                  callisto
+
+OSFlavour:                                 ubuntu
+OSVersion:                                 22.04
+Kernel:                                    5.19.0-46-generic
+
+CPUModel:                                  Intel(R) Core(TM) i7-4558U CPU @ 2.80GHz
+CPUName:                                   i7-4558U
+CPUSockets:                                1
+CPUCoresPerSocket:                         2
+CPUThreadsPerCore:                         2
+Cores:                                     2
+Threads:                                   4
+
+ROOTVersion:                               6.28/04
+Geant4Version:                             10.2.3
+
+MEGAlibVersion:                            3.99.02
+MEGAlibGitHash:                            08b49f84e201ebaf3691011a9fceaec3c65daaa5 2023-07-10
+MEGAlibOptimization:                       -O -DNDEBUG
+
+# Cosima
+DurationCosimaSingle:                      36.294
+EventsPerSecondCosimaSingle:               2755.276
+DurationCosimaMultiple:                    63.256
+EventsPerSecondCosimaMultiple:             6323.510
+
+# Revan
+DurationRevanSingle:                       8.409
+EventsPerSecondRevanSingle:                11892.020
+DurationRevanMultiple:                     12.547
+EventsPerSecondRevanMultiple:              31880.130
+
+# ResponseCreator
+DurationResponseCreatorSingle:             18.994
+EventsPerSecondResponseCreatorSingle:      5264.820
+DurationResponseCreatorMultiple:           42.131
+EventsPerSecondResponseCreatorMultiple:    9494.196
+
+# MimrecImaging
+DurationMimrecImagingSingle:               70.112
+EventsPerSecondMimrecImagingSingle:        1426.289
+DurationMimrecImagingMultiple:             33.153
+EventsPerSecondMimrecImagingMultiple:      3016.318
+

resource/examples/benchmarks/References/io.bm

@@ -0,0 +1,47 @@
+# Benchmark summary file
+
+HostName:                                  io
+
+OSFlavour:                                 macOS
+OSVersion:                                 13.4.1
+Kernel:                                    22.5.0
+
+CPUModel:                                  Intel(R) Core(TM) i5-2415M CPU @ 2.30GHz
+CPUName:                                   i5-2415M
+CPUSockets:                                1
+CPUCoresPerSocket:                         2
+CPUThreadsPerCore:                         2
+Cores:                                     2
+Threads:                                   4
+
+ROOTVersion:                               6.28/04
+Geant4Version:                             10.2.3
+
+MEGAlibVersion:                            3.99.02
+MEGAlibGitHash:                            ab0bd75a1f7945060fbe97ed19a6e7209a7efb7d 2023-07-10
+MEGAlibOptimization:                       -O -DNDEBUG
+
+# Cosima
+DurationCosimaSingle:                      68.194
+EventsPerSecondCosimaSingle:               1466.404
+DurationCosimaMultiple:                    118.714
+EventsPerSecondCosimaMultiple:             3369.442
+
+# Revan
+DurationRevanSingle:                       19.238
+EventsPerSecondRevanSingle:                5198.045
+DurationRevanMultiple:                     18.737
+EventsPerSecondRevanMultiple:              21348.134
+
+# ResponseCreator
+DurationResponseCreatorSingle:             33.686
+EventsPerSecondResponseCreatorSingle:      2968.592
+DurationResponseCreatorMultiple:           65.550
+EventsPerSecondResponseCreatorMultiple:    6102.212
+
+# MimrecImaging
+DurationMimrecImagingSingle:               103.211
+EventsPerSecondMimrecImagingSingle:        968.888
+DurationMimrecImagingMultiple:             48.047
+EventsPerSecondMimrecImagingMultiple:      2081.295
+